Visualizing output from TopHat and BowTie

The image below shows output from TopHat and BowTie, programs that align short reads from Illumina sequencing experiments onto a genome. The top two tracks are from a BED format file that TopHat creates in which each line of the BED file represents a splicing choice and the score field indicates the number of reads that supported that choice. The two floating graphs (red and green) are from WIG files the programs produce that summarize the number of reads covering individual regions. In this particular experiment, the control sample (green) produced many more reads than the treatment sample (red), and so the fact that there are more reads overall in the treatment (red) sample tells us this gene is up-regulated under the treatment.